Making edges "square" for 3D printing
Sounds like you want to keep your horizontal/vertical edges perfectly horizontal or vertical?  If so you can use Blender's snapping tools to make sure that vertices line up perfectly.  If you don't want to snap individual vertices, you can use the 'Mesh Edit Tools 2' add-on that comes with Blender...no need to download or purchase or anything; it should be there already:



Enable it and you'll get an additional section in your toolbox:



Under 'Vertex' select the dropdown and choose 'Custom Coordinates':



Then select the vertices you want to align, like this exaggerated example:



Choose 'Align Coordinates' and type in the value to align to.  In my example, it's just z = 1.0:



Click 'Ok', and boom, all of the vertices are now EXACTLY at z = 1.0:



Obviously you'll need to figure out the values to square to, but this should give you perfectly straight and square prints if you take the time to align the vertices on your edges.